HNCDB - a powerful database platform for head and neck tumors.

Head and neck cancer (HNC) is the sixth most common cancer in the world.
over the past decade, it has accumulated a large amount of annotation of genetic and pharmaceutical data for HNC.
, however, it is time-consuming and labor-consuming to gradually look for relevant genes and drugs through literature.
Therefore, a research team from Sun Yat-sen University Cancer Prevention and Control Center in China has constructed HNCDB, a database of head and neck cancer, which is constructed by integrating the document text mining of PubMed abstracts and collecting high-volume gene expression data of HNC from geo and TCGA databases, and manually organizing a large number of texts to collect reliable information about HNC-related genes and drugs.
: The database consists of three main analysis modules: Gene, Connectivity Map, and Analysis.
01 Gene contains comprehensive information on 1,173 HNC-related genes compiled from 2,564 publications, allowing you to find information about the genes you study efficiently and accurately in a short period of time.
02 Connectivity Map includes information about the potential link between 176 drugs artificially curated from 2,032 publications and 1,173 HNC-related genes.
03 Analysis we were used to analyze correlation, differential expression, and survival of 2,403 samples from 78 HNC gene expression datasets.
it's rare and precious to manually collate relevant information from so much data, so let's see how this powerful database can be used? Enter the URL and go to HomePartI. Gene in addition to downloading the NCBI GEO microarray expression dataset and clinical data, this section also collects the process expression data of TCGA samples from the Broad Institute's Firehose and TANRIC databases.
can be viewed here in the tumor tissue vs. normal tissue comparative data analysis or HPV negative and positive comparative analysis results, heat map behavior and HNC-related genes, listed as HNC-related drugs.
cell in the heat map has a score that represents the contract strength of the gene-drug pair.
addition, the number of PubMed abstracts containing HNC-related genes and drugs is shown in the first and second columns, respectively.
click on the number, we can view the details of the paper discussing the gene or drug of interest, and we can also analyze it by searching the search box for the gene or drug of interest.
click on any data box to see the details: 1 Gene Basics By clicking on the heat map cell, we can get more information about the connection between the selected gene and the drug.
2 gene-related report bar chart will show how the gene is studied in the literature, including down, phosphorylation, amplification, mutation, and so on.
the table below will provide more detailed information about the source of the literature, the methods used to study gene expression, and the role of the gene in head and neck cancer.
if you find a document of interest, click on the second link and go directly to the article's home page.
3 gene expression can be analyzed here for differences in the expression of the gene in head and neck cancer and in normal groups, and you can see the details by moving the mouse over the box chart.
data source 4 survival analysis shown above shows the survival analysis of the gene against head and neck cancer in different data sets, with red representing high expression and blue representing low expression.
the PartII. Drug Life Map gene and drug-related heat map: We can search the text box for specific HNC-related genes or HNC-related drugs.
, the darker the redness, the stronger the correlation between the drug and the gene.
the cell to get basic information about HNC-related genes and selected drugs from DrugBank.
include the type of drug, half-life, mechanism of action, related other targets, etc.
Part III. Analysis consists of three parts: difference analysis, correlation analysis, and survival analysis.
where we can perform interactive analysis of 2,403 HNC samples collected from the GEO and TCGA databases.
1 Difference Expression Analysis We may choose to perform differential expression analysis between HPV-positive and HPV-negative or Tumor and Normal HNC samples.
select a dataset type and gene type, click on the submit heat map to show the genes expressed significantly differently in the selected dataset, red for HPV-positive, blue for HPV-negative, and darker the color difference, the more significant.
other datasets to get different results, click Show Result Table to display details including logFC, AveExpr, P.Value, adj. P.Val, there is too much data to retrieve the desired gene in the upper right search box.
click on the gene in the table, you can pop up the difference in the high ground expression of the gene in the two sets of data, and move the mouse over the box chart to display the relevant numerical information.
2 correlation analysis select the Correlation Analysis option to first enter the two genes that we want to perform the expression-related analysis.
select the dataset to participate in the analysis.
click "Submit" and wait a minute.
Take EGFR and CD80 as examples, the correlation results are shown in the form of scatter charts, double-click dots can delete this point, scatters will automatically adjust the size of the adapted view, simple and convenient operation, so that the results of the graph more beautiful.
3 Survival Analysis Click Survival Analysis option where we can obtain the results of a single variable Cox proportional risk regression analysis to assess the relationship between survival and target gene expression.
first enter a gene in the text box for survival analysis.
you want to study multiple genes, you can enter a list of genes into the text box in Multigene Expression Survival Analysis and click Submit for survival analysis.
The function of the database is introduced here is over, this database combines TCGA and GEO two databases of cancer sequencing data, and comprehensively combined with literature information to provide HNC-related drugs, is a powerful tool for pre-experimental selection of targeted drugs, screening related genetic markers, the database can also carry out differential analysis, survival analysis, correlation analysis, etc. , is the head and neck cancer-related research researchers can use this database to send a good bioinscerology article.
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